centWave Parameters

ppm, peakwidth, snthresh, prefilter, mzCenterFun, integrate, mzdiff, fitgauss, scanrange, noise.

All centWave parameters require fine-tuning for each assay type and mass analyser.

The following illustrates all xcms parameters.

Explanation of parameters:

Parameter Explanation Pre-adjusted value
ppm signal deviation in m/z dimension 25
peakwidht range peak elution times in seconds 20-50 s
snthresh signals below this locally defined value are not considered as signals 10
prefilter Peak definition: how many data points (n) should be above a certain intensity threshold (I) k=3, I=100
mzdiff Closeness of two signals in mz dimension -0.001
noise Intensity threshold, values below are considered instrument noise 0
integrate Integration method: 1 - Mexican hat filtered data (less exact), 2- real data (prone to noise) 1
mzCenterFun Function to calculate m/z center of chromatographic peak weighted Mean (wMean)
fitgauss Peak fitting using Gauss distribution FALSE

ppm

mzdiff

noise

snthresh

peakwidth

prefilter